Sorry, rewriting the whole answer, as I remember what I needed to do and which should fix your problem.
Check the .htaccess file in the top-level directory, I added exceptions for js/css/imagesdirs, otherwise they would be rewritten:
RewriteEngine on
RewriteCond $1 !^(index\.php|css|images|js|robots\.txt)
RewriteRule ^(.*)$ /index.php/$1 [L]
source
share